Analyze Nucleotides or Amino Acids?

Nucleotides

Do you have a Multiple Sequence Alignment (MSA) to upload?

YES
NO

Upload your Multiple Sequece Alignment file:

ConSurf accepts external MSAs in the 7 formats supported by CLUSTAL W. These are: NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF and RSF format. In case you provide an external MSA file in Fasta format, please use the "-" sign as the only gap symbol, as this is the only standard gap sign that ConSurf accepts.

AND
Indicate the Query Sequence Name:

This should be the exact name of the sequence in the provided MSA file, that corresponds to the query protein.

Choose parameters to build the Multiple Sequence Alignment (MSA)

Alignment program

Nucleotides Database

SwissProt - a curated protein sequence database which strives to provide a high level of annotationClean UniProt - a modified version of the UniProt database aimed to screen the more reliable sequences.UniRef90 - database cluster sequences and sub-fragments with 11 or more residues that have at least 90% sequence identity with each other (from any organism) into a single UniRef entry, displaying the sequence of a representativeUniProt is the universal protein resource, a central repository of protein data created by combining Swiss-Prot, TrEMBL and PIR.

Maximum Homologs to collect

The maximum number of homologues, from those found by PSI-BLAST (with the given E-value), to be included in the calculation. In order to include all the homologues, replace the default value with the word "all".

Maximal %ID Between Sequences

Filter out redundant sequences. Sequences are clustered according to the given sequence identity cutoff, one representative of each cluster is reserved.

Minimal %ID For Homologs

Minimal sequence identity with the query sequence. Blast hits that shares less than the given identity cutoff are ignored

BLAST E-value Cutoff

Let me select the sequences for the analysis manually out of Blast results

Do you have a Tree file to upload?

YES
NO

Upload your TREE file (in Newick format):

In case you provide an external multiple sequence alignment (MSA) file, ConSurf can also accept a corresponding external phylogenetic tree in Newick (Phylip) format, for example: Tree File. The names of the proteins sequences in the tree file must be identical to the names in the MSA file.

Calculation Method

The calculation method for the rate of evolution at each site in the MSA. The Bayesian method was shown to significantly improve the accuracy of conservation scores estimations over the Maximum Likelihood method, in particular when a small number of sequences are used for the calculations. An additional advantage of the Bayesian method is that a confidence interval is assigned to each of the inferred evolutionary conservation score.